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This research aims to produce a valid and practical barcode-based three-dimensional learning media for primary schools and have the effectiveness on learning outcomes in learning Science. The module based on website was developed through three stages, namely needs analysis, design/planning stage, development and implementation stage. To view its validity had evaluated by experts, to look at its practicalities had used one-on-one evaluation and small groups- evaluation, while to look at the effective had used field test and student-s activity. The results showed that the evaluation of experts amounted to 4.27 with very valid criteria, the results of questionnaires student response data showed an average of 76%. Learning outcomes with score gain score of 0.78 with high category. Students activity is 85.4% with very good criteria. The development of three-dimensional based learning media developed has been valid, practical, and has effectiveness on student learning outcomes and activeness.